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EP2904119B1 - Verfahren für mit dem dna-erfassungspfad assoziierten leiden - Google Patents

Verfahren für mit dem dna-erfassungspfad assoziierten leiden Download PDF

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EP2904119B1
EP2904119B1 EP13844520.0A EP13844520A EP2904119B1 EP 2904119 B1 EP2904119 B1 EP 2904119B1 EP 13844520 A EP13844520 A EP 13844520A EP 2904119 B1 EP2904119 B1 EP 2904119B1
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dna
inhibitor
artificial sequence
synthetic polynucleotide
cells
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EP2904119A4 (de
EP2904119A1 (de
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Mark Nackyoung LEE
Nir Hacohen
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General Hospital Corp
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General Hospital Corp
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    • A61K31/7088—Compounds having three or more nucleosides or nucleotides
    • A61K31/713—Double-stranded nucleic acids or oligonucleotides
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    • A61K31/19—Carboxylic acids, e.g. valproic acid
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    • A61K31/505—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
    • A61K31/506—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim not condensed and containing further heterocyclic rings
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    • A61K31/635—Compounds containing para-N-benzenesulfonyl-N-groups, e.g. sulfanilamide, p-nitrobenzenesulfonyl hydrazide having a heterocyclic ring, e.g. sulfadiazine
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Definitions

  • the innate immune system detects viral infection primarily by recognizing viral nucleic acids inside an infected cell.
  • retroviruses which are RNA viruses that replicate via a DNA intermediate
  • the reverse transcribed DNA is believed to be recognized during entry into a host cell by a cytoplasmic DNA sensor(s) that triggers type I IFN production.
  • cytoplasmic DNA sensor(s) that triggers type I IFN production.
  • This latter response has been observed in cells that lack the endoplasmic reticulum (ER)-associated 3'->5' exonuclease, TREX I.
  • TREX1 When TREX1 is present, it can degrade the viral DNA before sensing occurs.
  • the invention relates broadly to monitoring and modulation of DNA sensing pathways and concomitant innate immune responses for diagnostic and therapeutic purposes.
  • the invention is premised in part on a more complete understanding of the mechanisms involved in DNA sensing pathways which in turn has led to a more complete understanding of the mechanism involved in DNA-triggered innate immune response induction.
  • novel components of the DNA sensing pathway were identified. These novel components include ABCFI, HSP90, and CDC37. TBKI was also found to be involved in the DNA sensing pathway.
  • the invention therefore provides an ABCF1 inhibiting siRNA for use in the treatment of disease in accordance with claim 1.
  • the invention contemplates treatment of the conditions specified in claim 1 using siRNA inhibitors of ABCF I, optionally together with inhibitors of HSP90, CDC37 and/or TBK.
  • the invention provides insight into the upstream events involved in DNA-triggered immune response induction. In this way, it identifies factors involved in these upstream events that can be targeted to prevent or reduce the underlying immune response. This is in contrast to the amelioration of symptoms resulting from the underlying immune response. Accordingly, certain methods of the method are directed towards avoiding or reducing the immune response rather than dampening the symptoms of the immune response.
  • the disclosure concerns a method comprising measuring presence or level of a DNA sensing pathway marker in a subject, and administering to a subject having an aberrant level of the DNA sensing pathway marker an effective amount of an active agent selected from the group consisting of an ABCF1 inhibitor, an HSP90 inhibitor, and a CDC37 inhibitor, or a combination thereof.
  • the disclosure concerns a method comprising administering to a subject, identified as having an aberrant level of a DNA sensing pathway marker, an effective amount of an active agent selected from the group consisting of an ABCF1 inhibitor, an HSP90 inhibitor, and a CDC37 inhibitor, or a combination thereof.
  • the method further comprises administering a TBK1 inhibitor to the subject.
  • a TBK1 inhibitor to the subject.
  • the result is a synergistic effect (i.e., the effect is more than additive).
  • the DNA sensing pathway marker is aberrant interferon-stimulated gene (ISG) expression, a mutation in Trex 1, Dnase1 , Dnase2, Fen1 (DnaseIV), RnaseH2, SAMHD1, or another nuclease, reduced expression of Trex 1, Dnase1, Dnase2, Fen1 (DnaseIV), RnaseH2, SAMHD1, or another nuclease, or reduced activity of Trex 1, Dnase1, Dnase2, Fen1 (DnaseIV), RnaseH2, SAMHD1, or another nuclease.
  • ISG interferon-stimulated gene
  • Aberrant (ISG) expression may be mRNA expression or protein expression and thus may be measured at the mRNA level and/or the protein level.
  • Aberrant ISG expression is an expression of an interferon-stimulated gene (ISG) that is abnormal. Such expression is above the normal expression level ofISG. In some instances, that abnormal level is simply presence of ISG expression where in a normal setting such expression is absent. ISGs are known in the art as evidenced by de Veer et al. J Leukoc Biol, 2001, 69(6):912-20 .
  • Examples include IRF J , C6orfl 50 (also known as MB21Dl ), HPSE, RIG-I (also known as DDX58), MDA5 (also known as IFIHI) and IFITM3, DDX60, IFI44L, IFI6, IFITM2, MAP3Kl 4, MOVJ O, NAMPT (also known as PBEF J), OASL, RTP4, TREXJ and UNC84B (also known as SUN2).
  • the active agent is an ABCF 1 inhibitor siRNA.
  • An example is the siRNA sc-140760.
  • the active agent comprises an HSP90 inhibitor.
  • the active agent comprises a CDC37 inhibitor.
  • the active agent is administered together with a TBK1 inhibitor.
  • a CDC37 inhibitor and an HSP90 inhibitor are used together (i.e., two separate and different active agents are administered to the subject) with an ABCF1 inhibitor.
  • three inhibitors of different classes are administered to the subject (e.g., an HSP90 inhibitor, a CDC37 inhibitor, and a TBK1 inhibitor) together with an ABCF1 inhibitor.
  • the HSP90 inhibitor is 17-DMAG, 17-AAG, or geldanamycin.
  • the CDC37 inhibitor is celastrol.
  • the TBK1 inhibitor is BX795 or MRT67307.
  • the active agent is administered prior to the onset of symptoms associated with an autoimmune disorder.
  • the active agent(s) is administered at regular intervals (or chronically) to the subject (e.g., daily, weekly, monthly) in order to prevent the onset or occurrence of the immune response.
  • the active agent(s) may be administered more regularly during certain times, including for example when exposure to stimuli of the immune response is most prevalent.
  • the disclosure concerns a method for treating a subject having Aicardi-Goutieres syndrome (AGS) comprising administering to said subject an effective amount of an ABCF1 inhibitor, an HSP90 inhibitor, or a CDC37 inhibitor, or a combination thereof.
  • AGS Aicardi-Goutieres syndrome
  • the disclosure concerns a method for treating a subject having familial chilblain lupus (FCL) comprising administering to said subject an effective amount of an ABCF1 inhibitor, an HSP90 inhibitor, or a CDC37 inhibitor, or a combination thereof.
  • FCL familial chilblain lupus
  • the disclosure concerns a method for treating a subject having retinal vasculopathy with cerebral leukodystrophy (RVCL) comprising administering to said subject an effective amount of an ABCF1 inhibitor, an HSP90 inhibitor, or a CDC37 inhibitor, or a
  • the subject carries a mutation in Trex 1, Dnase 1, Dnase2, Fen1 (DnaseIV), RnaseH2, SAMHD I, or another nuclease, or manifests aberrant interferon-stimulated gene (ISG) expression or reduced expression of Trex 1, Dnase1 , Dnase2, Fen1 (DnaseIV), RnaseH2, SAMHD I or another nuclease, or reduced activity of Trex 1, Dnase1, Dnase2, Fen1 (DnaseIV), RnaseH2, SAMHD I, or another nuclease.
  • ISG interferon-stimulated gene
  • the disclosure concerns a method for stimulating an immune response in a subject comprising administering to a subject an effective amount of a PTPN I inhibitor, a PPP6C inhibitor, or a combination thereof.
  • the subject has a viral infection.
  • the viral infection is a retroviral infection.
  • the retroviral infection is an HIV infection.
  • the viral infection is an infection with a DNA virus.
  • the DNA virus is HSV.
  • the subject has cancer.
  • the PTPN I inhibitor, or the PPP6C inhibitor, or a combination thereof is used in combination with a DNA vaccine.
  • the immune response is an innate immune response.
  • the PTPN I inhibitor is 3-(3,5-Dibromo-4-hydroxy-benzoyl)-2-ethyl-benzofuran-6-sulfonicacid-(4-(thiazol-2-ylsulfamyl)-phenyl)-amide.
  • the PTPN I inhibitor may be an siRNA.
  • the PPP6C inhibitor may be an siRNA.
  • the invention is premised, in part, on the identification of novel components of a signaling pathway that mediates innate immune responses triggered by the presence of cytosolic DNA.
  • This pathway is referred to herein as the "DNA sensing pathway”.
  • These newly discovered components can be targeted in order to modulate the DNA sensing pathway and the innate immune response it triggers.
  • the invention therefore provides methods for modulating the DNA sensing pathway with the aim of also modulating the innate immune response activated by the pathway as a result of the presence of cytosolic DNA.
  • Certain methods of the invention modulate other immune responses in addition to those responses triggered by the DNA sensing pathway. That is, some methods provided herein modulate the RNA sensing pathway as well the DNA sensing pathway.
  • the invention contemplates down-regulating the DNA sensing pathway thereby reducing, in whole or in part, or preventing the occurrence of the downstream innate immune response.
  • the invention contemplates down-regulating the innate immune response that is downstream of the DNA sensing pathway by targeting intermediate components in the overall pathway.
  • Such down-regulation would be useful in aberrant immune responses that are triggered by the presence of DNA (such as cytosolic DNA).
  • DNA such as cytosolic DNA
  • the presence of cytosolic DNA may be the result of a mutation in a nuclease that normally functions to prevent the accumulation of DNA in the cytosol.
  • An example of such a nuclease is TREX I.
  • nucleases involved in preventing accumulation of nucleic acids in the cytosol examples include DnaseI, Dnase2, Fenl (DnaseIV), RnaseH2, and SAMHDI.
  • Subjects having such nuclease mutations are more likely to develop aberrant immune responses due to the inappropriate presence of DNA. In some instances, the subjects have or are at risk of developing an autoimmune disorder. Of particular interest are the autoimmune disorders AGS, FCL, and RVCL. Also of interest are subjects having a nuclease mutation and, for example, a retroviral infection.
  • the invention may be used to treat subjects identified through the presence of or an abnormal level of a DNA sensing pathway marker.
  • the invention provides a personalized medicine approach.
  • the ability to identify subjects having an overactive DNA sensing pathway allows a medical practitioner to treat only that subset of subjects that is considered most likely to respond beneficially to the treatments contemplated herein.
  • This tailored treatment strategy avoids administering ineffective agents to subjects, many of whom are severely ill, without therapeutic benefit and in some cases with unwanted and perhaps unacceptable side effects.
  • the invention therefore contemplates that not all autoimmune disorders are associated with an aberrant DNA sensing pathway and that only those associated with such an aberrant pathway should be treated using the methods of the invention.
  • EAE an experimental model system of human autoimmune disorder, is not associated with an aberrant DNA sensing pathway.
  • Such markers include mRNA or protein levels of interferon or interferon-stimulated gene (collectively, referred to as ISG) in for example monocytes-derived dendritic cells, skin fibroblasts or blood cells, particularly following stimulation with transfected DNA or a retrovirus, levels of interferon proteins in peripheral blood serum or cerebrospinal fluid, and presence of nuclease mutations such as Trex 1 mutations, Dnasel mutations, Dnase2 mutations, Fenl mutations, RnaseH2 mutations and SAMHD I mutations. It is to be understood that such markers may also be used to diagnose an aberrant DNA sensing pathway. As used herein, an aberrant DNA sensing pathway is an overactive DNA sensing pathway.
  • any of the markers set forth herein may be used to determine if a subject has an aberrant or overactive DNA sensing pathway. This diagnosis may be performed in a subject who is asymptomatic. Certain methods of the invention therefore include a step of identifying a subject having an aberrant DNA sensing pathway following by a step of treating the subject with a particular inhibitors.
  • the invention contemplates the use of ABCFI inhibitors, HSP90 inhibitors, and/or CDC37 inhibitors, alone or in combination, including any combination thereof for down-regulating innate immune responses. These inhibitors are discussed in greater detail herein. These inhibitors may be used in combination with TBK I inhibitors.
  • the level (e.g., gene or protein level) of HSP90, CDC37, ABCF I and optionally TBKI is normal in the subject (or in cells obtained from the subject). Accordingly, in some embodiments, subjects having normal levels of HSP90, CDC37, and/or ABCF 1, and optionally TBKI are intended to be treated by the methods of the invention using the classes of inhibitors taught herein.
  • the HSP90 inhibitor is an agent that binds to HSP90 protein and interferes with its binding to CDC37.
  • the HSP90 inhibitor may not interfere with the ATP-binding activity of HSP90, in some embodiments.
  • the CDC37 inhibitor is an agent that binds to CDC37 protein and interferes with its binding to HSP90.
  • the disclosure concerns up-regulating the DNA-triggered innate immune response in order to provide a more robust immune response in a subject. Such upregulation would be useful in instances where the DNA-triggered immune response is beneficial and it is desirable to increase the level of that response. As an example, it may be desirable to up-regulate an immune response in the context of infections such as certain viral infections and certain bacterial infections, in an environment of dying cells including dying tumor cells, dying infected cells, and the like, and in the context of DNA vaccines.
  • the disclosure concerns the use of PTPN I and PPP6C inhibitors, alone or in combination, to up-regulate the innate immune response. These inhibitors are discussed in greater detail herein. The finding that inhibition of these signaling pathway components would up-regulate the immune response was unexpected.
  • Innate immunity which is also known in the art as natural or native immunity, is an immune response that involves neutrophils, granulocytes, mononuclear phagocytes, dendritic cells, NKT cells, and NK cells.
  • Innate immune responses can include, without limitation, type I interferon (such as IFN-alpha and IFN-beta) production, neutrophil activation, macrophage activation, phagocytosis, opsonization, complement activation, and any combination thereof.
  • type I interferon such as IFN-alpha and IFN-beta
  • the invention contemplates the use of inhibitors of one or more components of the DNA sensing pathway in order to down-regulate or up-regulate innate immune responses.
  • Inhibitors that down-regulate the innate immune response may be used individually or in combination.
  • inhibitors that up-regulate the innate immune response may be used individually or in combination.
  • ABCF I (ATP-binding cassette sub-family F member 1) is a 845 amino acid protein encoded by the human gene ABCF 1.
  • the human homolog of ABCF 1 is also known as ABC50 and ABC27, and the murine homolog is also known as Abc50, GCN20, AU41969 and DI 7Wsu166e in mouse. Nucleotide and amino acid sequences can be found at GenBank Accession No. NM 001025091.1 for human ABCF I and NM 013854.1 for mouse ABCFI.
  • ABCF I belongs to the ABC transporter family (EF3 subfamily) and contains two ABC transporter domains. ABC proteins are thought to transport various molecules across extra- and intra-cellular membranes.
  • an ABCF I inhibitor is an agent that inhibits ABCFI activity.
  • the inhibitor can be nucleic acid or amino acid in nature, and in some important embodiments it is a chemical compound, whether organic or inorganic in nature.
  • the inhibitor may prevent or reduce the synthesis of ABCFI for example by blocking its mRNA or protein expression. Alternatively, it may reduce activity by interfering with ABCFI function, such as by binding by ABCFI and thereby interfering with its ability to bind DNA, or HMGB2, IFI16 or other proteins.
  • Antibodies that bind to ABCF I are described in U.S. Patent No. 7,612,181 .
  • U.S. Patent No. 7,482,334 also provides compounds that may be used in the invention as inhibitors of ABCFI. Reference may also be made to U.S. Patent Nos. 7,910,571 , 7,935,839 , and 7,547,687 .
  • a HSP90 inhibitor is an agent that inhibits HSP90 activity.
  • the inhibitor can be nucleic acid or amino acid in nature, and in some important embodiments it is a chemical compound, whether organic or inorganic in nature.
  • the inhibitor may prevent or reduce the synthesis of HSP90 for example by blocking mRNA or protein expression. Alternatively, it may reduce activity by interfering with HSP90 function, such as by binding by HSP90 and thereby interfering with its ability to bind ATP or other proteins.
  • HSP90 inhibitors which can be used with the methods of the present invention include, but are not limited to, quinone ansamycin antibiotics, such as the macbecins, geldanamycin, including derivatives of geldanamycin, such as 17-(allylamino)-17-desmethoxygeldanamycin (17-AAG), its dihydro derivative, 17-AAGH 2 , and 17-amino derivatives of geldanamycin such as 17-dimethylaminoethylamino-17-demethoxy-geldanamycin (17-DMAG), 11-oxogeldanamycin, and 5,6-dihydrogeldanamycin, which are disclosed in U.S. Pat. Nos. 4,261,989 ; 5,387,584 ; and 5,932,566 .
  • Another HSP90 inhibitor is ganetespib.
  • HSP90 inhibitors include radicicol and oximes and other analogs thereof, disclosed in Soga, et al., Curr. Cancer Drug Targets, 3, 359-69 (2003 ), and in Yamamoto, et al., Angew. Chem., 42, 1280-84 (2003 ); and in Moulin, et al., J. Amer. Chem. Soc., vol 127, 6999-7004 (2005 ); purine derivatives such as PU3, PU24FCI and PUH64 (see Chiosis et al., ACS Chem. Biol. Vol. 1(5), 279-284 (2006 ) and those disclosed in PCT Application No.
  • HSP90 inhibitors include novobiocin analogues, as provided by U.S. Patent 7,622,451 Further examples of HSP90 inhibitors include dexamethasone and benzoquinone ansamycins such as those described in U.S. Pat. No. 6,872,715 .
  • HSP90 inhibitors include herbimycin A and other synthetic compounds that can bind into the ATP-binding site of HSP90, as disclosed by U.S. Pat. No. 7,211,562 .
  • Antibodies or antibody fragments that selectively bind to HSP90 may also be administered as drugs to cause inhibition of HSP90, and can be used in combination with the compounds of the invention.
  • Nucleotide and amino acid sequences can be found using GenBank Accession No. NM_005348.2 for human Hsp90AA1, NM_007355.2 for human Hsp90AB1, NM_010480.5 for mouse Hsp90AA1, and NM_008302.3 for mouse Hsp90AB 1.
  • a CDC37 inhibitor is an agent that inhibits CDC37 activity.
  • the inhibitor can be nucleic acid or amino acid in nature, and in some important embodiments it is a chemical compound, whether organic or inorganic in nature.
  • the inhibitor may prevent or reduce the synthesis of CDC37 for example by blocking mRNA or protein expression. Alternatively, it may reduce activity by interfering with CDC37 function, including interaction with its partner HSP90.
  • CDC37 inhibitor An example of a CDC37 inhibitor is celastrol.
  • Celastrol has been reported to be an HSP90 inhibitor in the art. However, the findings provided herein indicate that it binds to CDC37 and may inhibit HSP90 only indirectly (e.g., by preventing the binding of HSP90 to CDC37.
  • Nucleotide and amino acid sequences can be found using GenBank Accession No. NM_007065.3 for human CDC37 and NM_016742.4 for mouse CDC37.
  • a TBK1 inhibitor is an agent that inhibits TBK1 activity.
  • the inhibitor can be nucleic acid or amino acid in nature, and in some important embodiments it is a chemical compound, whether organic or inorganic in nature.
  • the inhibitor may prevent or reduce the synthesis of TBK 1 for example by blocking mRNA or protein expression. Alternatively, it may reduce activity by interfering with TBK1 function, such as binding to and/or interfering with catalytic sites (e.g., kinase domain) or protein-protein interaction domains.
  • TBK1 inhibitors include, but are not limited to, MPI-0485520 (Myrexis, Inc.), BX 795 ( CAS No. 702675-74-9 , Axon Medchem BV), MRT67307 ( CAS No. 1190378-57-4 , Medchem Express), CYT387, as well as those disclosed in U.S. Pat. Nos. 8,263,139 ; 7,211,597 ; 7,186,743 ; 6,956,052 ; and 6,849,653 .
  • Nucleotide and amino acid sequences can be found using GenBank Accession No. NM_013254.3 for human TBK1 and NM_019786.4 for mouse TBKI.
  • a PTPN1 inhibitor is an agent that inhibits PTPN 1 activity.
  • the inhibitor can be nucleic acid or amino acid in nature, and in some important embodiments it is a chemical compound, whether organic or inorganic in nature.
  • the inhibitor may prevent or reduce the synthesis of PTPN 1 for example by blocking mRNA or protein expression. Alternatively, it may reduce activity by interfering with PTPN 1 function.
  • a PTPN 1 inhibitor is 3-(3,5-Dibromo-4-hydroxy-benzoyl)-2-ethyl-benzofuran-6-sulfonicacid-(4-(thiazol-2-ylsulfamyl)-phenyl)-amide.
  • a PPP6C inhibitor is an agent that inhibits PPP6C activity.
  • the inhibitor can be nucleic acid or amino acid in nature, and in some important embodiments it is a chemical compound, whether organic or inorganic in nature.
  • the inhibitor may prevent or reduce the synthesis of PPP6C for example by blocking mRNA or protein expression. Alternatively, it may reduce activity by interfering with PPP6C function.
  • siRNA shall refer to a particular type of isolated double-stranded ribonucleic acid (RNA) molecule characterized by a length of about 21-23 nucleotides, a single-stranded sense (s) strand and a single-stranded antisense (as) strand, wherein the antisense strand has a nucleotide sequence complementary to a target nucleotide sequence, which RNA molecule, when delivered into a cell expressing a protein encoded by the target sequence, reduces the amount of target nucleotide sequence (and the encoded protein) in the cell.
  • RNA ribonucleic acid
  • the sense and antisense strands of siRNA have nucleotide sequences which are strictly or at least substantially complementary to each other, such that they can form a stable duplex structure under suitable conditions, in vivo or in vitro.
  • one or both ends of either strand can extend beyond the corresponding end or ends of the other strand in the duplex structure, thereby allowing short overhanging sequence (generally 1-2 nucleotides long) at either or both ends of the siRNA.
  • the siRNA will generally include nucleotide subunits having canonical nucleobases common to RNA, e.g., adenine, cytosine, guanine, and uracil, but is not so limited. Other nucleobases, including but not limited to thymine and inosine, can also be present in some embodiments.
  • nucleotide sequence of a target is known, one of ordinary skill in the art is able to generate suitable siRNA that can inhibit protein production. Methods of generating siRNA to targets is known in the art.
  • the nucleotide sequences of the targets ABCF1, HSP90, CDC37 and TBK 1 provided herein and/or are known in the art.
  • the invention contemplates that the inhibitors of the invention may be small molecules.
  • small molecule is art-recognized and refers to a composition which has a molecular weight of less than about 2000 g/mole, or less than about 1OOO g/mole, and even less than about 500 g/mole.
  • Small molecules may include, for example, nucleic acids, peptides, peptide nucleic acids, peptidomimetics, carbohydrates, lipids or other organic (carbon containing) or inorganic molecules.
  • Many pharmaceutical companies have extensive libraries of chemical and/or biological mixtures, often fungal, bacterial, or algal extracts, which can be screened with any of the assays of the invention.
  • small organic molecule refers to a small molecule that is often identified as being an organic or medicinal compound, and does not include molecules that are exclusively nucleic acids, peptides, or polypeptides. In some cases, the small organic molecule is a pharmaceutically active agent (i.e., a drug).
  • a small molecule may be a non-peptidic, non-oligomeric organic compound either synthesized in the laboratory or found in nature.
  • Small molecules can refer to compounds that are "natural product-like", such as small molecule that are similar in structure to a natural product or are similar with respect to density of stereocenters, density of functional groups, ring systems, 3-D structure, etc. ; however, the term “small molecule " is not limited to "natural product-like” compounds and may include compounds that are not based on and are not similar to known natural products.
  • a small molecule may contain several carbon-carbon bonds, although this characterization is not intended to be limiting for the purposes of the present invention.
  • the disclosure concerns to diagnosing diseases associated with aberrant DNA sensing and/or identifying subjects to be treated based on the presence of one or more markers of aberrant DNA sensing.
  • Certain diagnostics for determining the presence of disease or identifying subjects with aberrant DNA sensing may include: (i) ex vivo stimulation of patient cells (monocyte-derived dendritic cells or skin fibroblasts) with transfected DNA or retrovirus, and measurement of interferon or interferon-stimulated gene (ISG) production; (ii) gene expression of blood cells to look for upregulation ofISGs; (iii) measurement of interferon proteins in peripheral blood serum or cerebrospinal fluid; (iv) stimulation of control cells with patient serum followed by measurement of ISG expression; (v) sequencing of Trex 1, Dnase1 , Dnase2, Fenl (DnaseIV), RnaseH2, SAMHD1 or other nucleases and nucleotidases to look for deleterious mutations that result
  • samples to be tested according to the foregoing methods may comprise cells and fluids from any region of the body, including but not limited to blood cells, skin cells, non-skin fibroblasts, and the like.
  • a marker of aberrant DNA sensing is a mutation in the Trex 1 gene locus.
  • a mutation in the Trex 1 gene locus refers to a mutation that reduces or eliminates synthesis of the TREX 1 protein or that encodes a TREX 1 protein with reduced or no nuclease activity. Mutations of interest include those that result in aberrant accumulation of cytosolic DNA, as compared to for example cells having no nuclease mutation. Mutations in the Trex 1 locus include point mutations, insertions, deletions, duplications, inversions, translocations, and the like. An example of such a mutation is a missense mutation that results in the amino acid substitution of D18N.
  • TREX1 amino acid substitutions such as R1 14H, A158V, G227S, A247P, R240S, P290L, Y305C, G306A, the frame shift (fs) mutations P212fs and D272fs, and the point deletion 979delC in the TREXJ 3' UTR. Additional TREX1 mutations are disclosed in published PCT application WO2008/03 7311 .
  • sequencing analysis may be performed on mRNA transcripts or cDNA counterparts (e.g., for coding region mutations) or on genomic DNA (for regulatory and/or coding region mutations).
  • regulatory regions are those nucleotide sequences (and regions) that control the temporal and/or spatial expression of a gene but typically do not contribute to the amino acid sequence of the gene product.
  • coding regions are those nucleotide sequences (and regions) that dictate the amino acid sequence of the gene product.
  • Assays that can identify protein abnormalities are known in the art and include enzyme-linked immunosorbent assay (ELISA) and other immunological detection methods such as Westerns.
  • nucleotide sequences of the human and mouse Trex 1 loci are provided in Table 1.
  • the invention contemplates identifying subjects having aberrant DNA sensing pathways and treating such subjects so identified using the methods provided herein. These subjects may have or may be at risk of developing an autoimmune disorder.
  • an autoimmune disorder is a disorder that results when a subject's immune system attacks its own organs or tissues, producing a clinical condition associated with the destruction of that tissue.
  • autoimmune disorders include but are not limited to systemic lupus erythematosus (SLE), rheumatoid arthritis, psoriatic arthritis, Type 1 immune-mediated or insulin-dependent diabetes mellitus, hemolytic anemias, rheumatic fever, Crohn's disease, Guillain-Barre syndrome, psoriasis, thyroiditis such as chronic thyroiditis and Hashimoto's thyroiditis, Grave's disease, myasthenia gravis, glomerulonephritis, polymyalgia, autoimmune hepatitis, temporal arteritis, cryoglobulinemia, multiple sclerosis, scleroderma, Wegener's granulomatosis, Addison's disease, autoimmune uveitis, autoimmune hemolytic anemia
  • the disclosure concerns methods for stimulating or enhancing an existing immune response in certain subjects under certain situations. Such situations include those in which the subject is in need of an immune response. As an example, the disclosure contemplates stimulating or enhancing an immune response in a subject that has or is at risk of developing an infection such as a viral infection. As another example, the disclosure contemplates stimulating or enhancing an immune response is a subject that has cancer or that was previously diagnosed with cancer and may be in remission. As yet another example, the disclosure contemplates stimulating or enhancing an immune response is a subject that is being vaccinated, including a subject being vaccinated with a DNA or RNA vaccine.
  • the disclosure contemplates administering to such subjects inhibitors of PTPN I or PPP6C, alone or in combination with each other, and optionally in combination with other active agents.
  • infectious microbe refers to an abnormal presence of an infectious microbe or infectious agent in a host.
  • An infection with an infectious microbe specifically includes a bacterial, viral, fungal, or parasitic infection, and any combination thereof.
  • a viral infection may be an infection by a DNA virus or an RNA virus.
  • DNA viruses are defined as viruses in which the genetic material is DNA rather than RNA.
  • the DNA may be either double- or single-stranded.
  • Illustrative DNA viruses include, but are not limited to, the family Poxyiridae, including the genus Orthopoxyirus (Variola major, Variolaminor, Monkey pox Vaccinia, Cowpox, Buffalopox, Rabbitpox, Ectromelia), the genus Leporipoxyirus (Myxoma, Fibroma), the genus Avipoxyirus (Fowlpox, other avian poxyirus), the genus Capripoxyirus (sheeppox, goatpox), the genus Suipoxyirus (Swinepox), the genus Parapoxyirus (contagious postular dermatitis virus, pseudocowpox, bovine papular stomatitis virus); the family Iridoviridae (African s
  • RNA viruses are viruses having genetic material that is RNA rather than DNA.
  • the RNA may be either double- or single-stranded.
  • Illustrative RNA viruses include, but are not limited to allexivirus genus, arenaviridae, arteriviridae, astroviridae, avsunviroidae, bamaviridae, benyvirus genus, bimaviridae, bomavirus genus, bromoviridae, bunyaviridae, caliciviridae, capillovirus genus, carlavirus genus, closteroviridae, comoviridae, coronaviridae, cricket paralysis virus genus, cystoviridae, deltavirus genus, enamovirus genus, filoviridae, flaviviridae, foveavirus genus, furovirus genus, hepatitis E-like virus genus, hordeivirus gen
  • Cancer refers to an uncontrolled growth of cells which interferes with the normal functioning of the bodily organs and systems. Cancers which migrate from their original location and seed vital organs can eventually lead to the death of the subject through the functional deterioration of the affected organs. Hemopoietic cancers, such as leukemia, are able to outcompete the normal hemopoietic compartments in a subject, thereby leading to hemopoietic failure (in the form of anemia, thrombocytopenia and neutropenia) ultimately causing death.
  • a metastasis is a region of cancer cells, distinct from the primary tumor location resulting from the dissemination of cancer cells from the primary tumor to other parts of the body.
  • the subject may be monitored for the presence of metastases. Metastases are most often detected through the sole or combined use of magnetic resonance imaging (MRI) scans, computed tomography (CT) scans, blood and platelet counts, liver function studies, chest X-rays and bone scans in addition to the monitoring of specific symptoms.
  • MRI magnetic resonance imaging
  • CT computed tomography
  • Cancers include, but are not limited to, basal cell carcinoma, biliary tract cancer; bladder cancer; bone cancer; brain and CNS cancer; breast cancer; cervical cancer; choriocarcinoma; colon and rectum cancer; connective tissue cancer; cancer of the digestive system; endometrial cancer; esophageal cancer; eye cancer; cancer of the head and neck; gastric cancer; intra-epithelial neoplasm; kidney cancer; larynx cancer; leukemia; liver cancer; lung cancer (e.g.
  • lymphoma including Hodgkin's and Non-Hodgkin's lymphoma; melanoma; myeloma; neuroblastoma; oral cavity cancer (e.g., lip, tongue, mouth, and pharynx); ovarian cancer; pancreatic cancer; prostate cancer; retinoblastoma; rhabdomyosarcoma; rectal cancer; renal cancer; cancer of the respiratory system; sarcoma; skin cancer; stomach cancer; testicular cancer; thyroid cancer; uterine cancer; cancer of the urinary system, as well as other carcinomas and sarcomas.
  • lymphoma including Hodgkin's and Non-Hodgkin's lymphoma
  • melanoma myeloma
  • neuroblastoma e.g., oral cavity cancer (e.g., lip, tongue, mouth, and pharynx)
  • ovarian cancer pancreatic cancer
  • prostate cancer retinoblastoma
  • DNA vaccines allow the direct injection of genetic material in the form of DNA, into a subject, thereby causing some cells to produce gene products from the introduced DNA. While not limiting the disclosure to one mechanism of action, it is contemplated that the gene products then illicit immune responses. DNA vaccines can produce robust immune responses in a variety of animal models as well as in humans, as exemplified in Donnelly, et al., Annu. Rev. Immunol. 15:617-648 (1997 ) and Manickan, et al., Crit. Rev. Immunol: 17(2):139-154 (1997 ).
  • the term "subject” refers to a human or non-human mammal or animal.
  • Non-human mammals include livestock animals, companion animals, laboratory animals, and non-human primates.
  • Non-human subjects also specifically include, without limitation, horses, cows, pigs, goats, dogs, cats, mice, rats, guinea pigs, gerbils, hamsters, mink, and rabbits.
  • a subject is referred to as a "patient.”
  • a patient or subject may be under the care of a physician or other health care worker, including, but not limited to, someone who has consulted with, received advice from or received a prescription or other recommendation from a physician or other health care worker.
  • treatment includes preventing a disease or condition from occurring (e.g., in a subject predisposed to such a disease or condition but not manifesting any symptoms associated therewith) or inhibiting a pre-existing disease or condition (e.g., either reducing the disease load or eliminating the disease altogether).
  • a disease or condition e.g., in a subject predisposed to such a disease or condition but not manifesting any symptoms associated therewith
  • a pre-existing disease or condition e.g., either reducing the disease load or eliminating the disease altogether.
  • the methods of the invention may also be used to reduce or ameliorate symptoms associated with the disease or condition.
  • an effective amount is any amount that can cause a beneficial change in a desired tissue.
  • an effective amount is that amount sufficient to cause a favorable phenotypic change in a particular condition such as a lessening, alleviation or elimination of the condition as a whole.
  • an effective amount is that amount of a pharmaceutical preparation that alone, or together with further doses, produces the desired response. This may involve only slowing the progression of the disease temporarily, although more preferably, it involves halting the progression of the disease permanently or delaying the onset of or preventing the disease or condition from occurring. This can be monitored by routine methods.
  • the effective amount is one that prevents the occurrence or onset of more than one, preferably the majority, and even more preferably all of the markers of the DNA-triggered innate immune response.
  • doses of active compounds would be from about 0.01 mg/kg per day to 1OOO mg/kg per day. It is expected that doses ranging from 50-500 mg/kg will be suitable, preferably orally and in one or several administrations per day.
  • Such amounts will depend, of course, on the particular condition being treated, the severity of the condition, the individual patient parameters including age, physical condition, size and weight, the duration of the treatment, the nature of concurrent therapy (if any), the specific route of administration and like factors within the knowledge and expertise of the health practitioner.
  • Lower doses will result from certain forms of administration, such as intravenous administration.
  • higher doses or effectively higher doses by a different, more localized delivery route
  • Multiple doses per day are contemplated to achieve appropriate systemic levels of compounds. It is preferred generally that a maximum dose be used, that is, the highest safe dose according to sound medical judgment. It will be understood by those of ordinary skill in the art, however, that a patient may insist upon a lower dose or tolerable dose for medical reasons, psychological reasons or for virtually any other reasons.
  • the agents of the invention may be combined, optionally, with a pharmaceutically-acceptable carrier to form a pharmaceutical preparation.
  • a pharmaceutically-acceptable carrier means one or more compatible solid or liquid fillers, diluents or encapsulating substances which are suitable for administration into a human.
  • carrier denotes an organic or inorganic ingredient, natural or synthetic, with which the active ingredient is combined to facilitate the application.
  • the components of the pharmaceutical compositions also are capable of being co-mingled with the molecules of the present invention, and with each other, in a manner such that there is no interaction which would substantially impair the desired pharmaceutical efficacy.
  • the pharmaceutical preparations comprise an agent of the invention in an amount effective to treat a disorder.
  • agents described herein may be used individually or together. When agents are used together (or in conjunction), they may be formulated and thus administered together or they may be formulated separately and administered together or separately.
  • the pharmaceutical preparations may contain suitable buffering agents, including: acetic acid in a salt; citric acid in a salt; boric acid in a salt; and phosphoric acid in a salt.
  • suitable buffering agents including: acetic acid in a salt; citric acid in a salt; boric acid in a salt; and phosphoric acid in a salt.
  • suitable preservatives such as benzalkonium chloride; chlorobutanol; parabens and thimerosal.
  • a variety of administration routes are available. The particular mode selected will depend, of course, upon the particular drug selected, the severity of the condition being treated and the dosage required for therapeutic efficacy.
  • the agents of the invention may be administered using any mode of administration that is medically acceptable, meaning any mode that produces effective levels of the active compounds without causing clinically unacceptable adverse effects.
  • modes of administration include oral, rectal, topical, nasal, interdermal, or parenteral routes.
  • parenteral includes subcutaneous, intravenous, intramuscular, or infusion. Intravenous or intramuscular routes are not particularly suitable for long-term therapy and prophylaxis.
  • pharmaceutical compositions for the acute treatment of subjects having a migraine headache may be formulated in a variety of different ways and for a variety of administration modes
  • compositions may conveniently be presented in unit dosage form and may be prepared by any of the methods known in the art of pharmacy. All methods include the step of bringing the active agent into association with a carrier which constitutes one or more accessory ingredients. In general, the compositions are prepared by uniformly and intimately bringing the active compound into association with a liquid carrier, a finely divided solid carrier, or both, and then, if necessary, shaping the product.
  • compositions suitable for oral administration may be presented as discrete units, such as capsules, tablets, lozenges, each containing a predetermined amount of the active compound.
  • Other compositions include suspensions in aqueous liquids or non-aqueous liquids such as a syrup, elixir or an emulsion.
  • compositions suitable for parenteral administration conveniently comprise a sterile aqueous preparation of the agents of the invention, which is preferably isotonic with the blood of the recipient.
  • This aqueous preparation may be formulated according to known methods using suitable dispersing or wetting agents and suspending agents.
  • the sterile injectable preparation also may be a sterile injectable solution or suspension in a non-toxic parenterally-acceptable diluent or solvent, for example, as a solution in 1,3-butane diol.
  • acceptable vehicles and solvents that may be employed are water, Ringer's solution, and isotonic sodium chloride solution.
  • sterile, fixed oils are conventionally employed as a solvent or suspending medium.
  • any bland fixed oil may be employed including synthetic mono-or di-glycerides.
  • fatty acids such as oleic acid may be used in the preparation of injectables.
  • Carrier formulation suitable for oral, subcutaneous, intravenous, intramuscular, etc. administrations can be found in Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, PA .
  • Other delivery systems can include time-release, delayed release or sustained release delivery systems. Such systems can avoid repeated administrations of the active compound, increasing convenience to the subject and the physician.
  • Many types of release delivery systems are available and known to those of ordinary skill in the art. They include polymer base systems such as poly(lactide-glycolide), copolyoxalates, polycaprolactones, polyesteramides, polyorthoesters, polyhydroxybutyric acid, and polyanhydrides. Microcapsules of the foregoing polymers containing drugs are described in, for example, U.S. Patent 5,075,109 .
  • Delivery systems also include non-polymer systems that are: lipids including sterols such as cholesterol, cholesterol esters and fatty acids or neutral fats such as mono-di-and tri-glycerides; hydrogel release systems; sylastic systems; peptide based systems; wax coatings; compressed tablets using conventional binders and excipients; partially fused implants; and the like.
  • Specific examples include, but are not limited to: (a) erosional systems in which the active compound is contained in a form within a matrix such as those described in U.S. Patent Nos. 4,452,775 , 4,675,189 and 5,736,152 , and (b) diffusional systems in which an active component permeates at a controlled rate from a polymer such as described in U.S. Patent Nos. 3,854,480 , 5,133,974 and 5,407,686 .
  • pump-based hardware delivery systems can be used, some of which are adapted for implantation.
  • Long-term sustained release means that the implant is constructed and arranged to delivery therapeutic levels of the active ingredient for at least 30 days, and preferably 60 days.
  • Long-term sustained release implants are known to those of ordinary skill in the art and include some of the release systems described above.
  • Ptpnl -1- MEFs and Ptpnl -1- MEFs rescued with Ptpnl cDNA were a gift from B.G. Neel ( Klaman et al., Mol Cell Biol, 2000, 20:5479-5489 ).
  • 293T cells were obtained from ATCC.
  • cDCs were prepared from B6.C3H-sst l (Spl 10 LoF) as previously described ( Altfeld et al., Nat. Rev. Immunol., 2011, 11: 176-186 ; Yan et al., Nat Immunol, 2010, 11: 1005-1013 ) .
  • Cells were maintained in DMEM (Mediatech) supplemented with 10% FBS (Sigma).
  • Human monocytes were isolated by negative selection (Life Technologies) from peripheral blood mononuclear cells, and differentiated into dendritic cells by a seven day culture in GM-CSF (R&D) and IL-4 (R&D) in RPMI (Life Technologies) supplemented with 10% FBS (Life Technologies).
  • Sendai virus was obtained from ATCC and used at an MOI of 1.
  • HSV-1 dl09 was obtained as a gift from N.A. DeLuca and was used at an MOI of 10 ( Samaniego et al., J Virol, 1998, 72: 3307-3320 ).
  • Self-inactivating minimal HIV-I virus was produced in 293T cells using the vector pLX301 (TRC, Broad Institute), the packaging construct psPAX2, and the envelope plasmid pCMV-VSVG.
  • Interferon stimulatory DNA (ISD), HIV gag-100, and HSV60 dsDNA were annealed from oligonucleotides (IDT) as described previously( Yan et al., Nat. Rev. Immunol., 2010, 11: 1005-1013 ; Stetson et al., Immunity, 2006, 24: 93-103 ; Unterholzner et al., Nat. Rev. Immunol., 2010, 11: 997-1004 ). Sequences are listed in -Table 1.
  • RNA In vitro transcribed RNA was synthesized as described previously ( Hornung et al., Science, 2006, 314: 994-997 ). Nucleic acids were mixed with Lipofectamine LTX (Life Technologies) at a ratio of 1:3 (wt/vol) in Opti-MEM (Life Technologies), and added to cells at a final concentration of 1 ug/mL (DNA) or 0.1 ug/mL (RNA) unless otherwise indicated. Recombinant IFN was obtained from PBL InterferonSource. Murine CXCL1O ELISA kit was obtained from R&D.
  • Antibodies were obtained from the following sources: anti-P-TBK I Serl72 (5483; Cell Signaling), anti-P-IRF3 Ser396 (4947; Cell Signaling), anti-TBKI (3504; Cell Signaling), anti-IRF3 (4302; Cell Signaling), anti-CDC37 (4793; Cell Signaling), anti-ABCFI (SAB2106638, Sigma), anti-HMGB2 antibody (ab67282, Abeam), anti-SET (sc25564, Santa Cruz), anti-IFI204 (SAB2105265, Sigma), anti-a-tubulin (T5168, Sigma), anti--actin (ab6276, Abeam), anti-HA (High Affinity 3F10; Roche), Anti-SMARCBI (H-300, Santa Cruz) and rat IgG control (Jackson Laboratories).
  • PTPN I inhibitor ( CAS 765317-72-4 ), okadaic acid, and celastrol were obtained from Millipore.
  • hypotonic lysis buffer (10 mM HEPES pH 7.4, 10 mM KCl, 1 mM EDTA) containing protease inhibitors (Roche) for 10 min on ice followed by lysis for 1 min in hypotonic lysis buffer supplemented with 0.3% Triton X-100. Nuclei and insoluble proteins were removed by centrifugation. 11 mg of the H and L lysates were mixed with a 1:1 mix of biotinylated ISD and ISD with a tetraethylene glycol arm between the biotin and the nucleic acid (IDT), and then split into two samples. No ISD was added to 11 mg of sample M.
  • Peptide extracts were cleaned up offline with C18 StageTips prior to 90 min nanoESI-LCMS analyses with a gradient of 3%-35% acetonitrile/ 0.1% formic acid.
  • Protein and peptide identification and quantification was performed with MaxQuant (v. 1.0.12.31) using the IPI mouse v3.52 as the search database.
  • Search parameters specified trypsin cleavage with 2 missed cleavages, peptide mass tolerance of 6 ppm and fragment mass tolerance of 0.5 Da; carbamidomethylated cysteines and variable modifications of oxidized methionine, acetylation of protein N-termini and sample-specific modifications of Arg-0,6,10 and Lys-0,4,8 for SILAC triple labeling.
  • Protein ratios were medians of ratios from at least two quantified peptides. To identify significant proteins, P-values were calculated via Gaussian modeling of the log(H/M) data, and a significance threshold of P ⁇ 1x1o- 4 was used.
  • Extracted peptides were purified with StageTips and analyzed with a 100 min acquisition method on a Thermo EASY-nLC 1OOO UHPLC coupled to a Q Exactive mass spectrometer.
  • Raw data files were processed in MaxQuant (v. 1.2.2.5) using the IPI mouse v3.68 as the search database.
  • All proteins were identified with at least 2 or more unique peptides and quantified with 3 or more ratios.
  • SILAC ratios were normalized over the median of all protein ratios to correct for sample losses between parallel immunoprecipitation steps. To identify significant interactions, P-values were calculated via Gaussian modeling of the log(M/L) and log(H/L) data, and a significance threshold of P ⁇ 0.01 was used.
  • RNA interference screen 750 p53- / - MEFs per well were seeded in 96-well plates in 60% DMEM and 40% Opti-MEM. 25 nM siRNA was complexed with 0.5 uL Lipofectamine RNAiMax (Life Technologies) in Opti-MEM, incubated for 12 min at 22°C, and added to the wells. 72 h later, cells were transfected with ISD. 26 h later, supematants were collected and CXCL1O was quantified by ELISA. Cell viability was estimated by the CellTiter-Glo Luminescent Cell Viability Assay (Promega); CellTiter-Glo values below 3.75e5 were considered toxic.
  • siRNAs were from Dharmacon, Life Technologies, Qiagen, and Sigma. siRNA sequences are listed in Table 1.
  • Plasmid construction To create the tet-on lentiviral vector (pCW57d-P2AR), the pLK0.1 ( Pichlmair et al., Nature, 2012, 487(7408):486-90 .) vector was modified as follows: the U6 shRNA cassette was removed from LK0.1 and the TRE with a MCS was inserted upstream of the PGK promoter; the rtTA was cloned 3' of the puroR (with a 2A multicistronic cleavage site between these two genes) along with a WPRE.
  • p53- / - MEFs stably expressing cDNA in the pCW57d-P2AR vector were subjected to siRNA. 72 h later, doxycycline (Sigma) at 0, 0.3, 3, or 30 ug/mL was added to the cells, and cells were stimulated with ISD. 26 h later, supematants were collected and CXCLIO was quantified by ELISA.
  • Rat IgG control bound to Protein G were used as IP control with the 48 h doxy-treated lysates.
  • the beads were washed extensively with wash buffer (10 mM Tris-HCl, 2 mM EDTA, 1% NP-40).
  • Immunoprecipitates were eluted with 100 uL 2.5 M Glycine (pH 3) and immediately buffered to pH 7.5 by adding 25 uL of 2 M Tris. Samples were boiled in reducing Laemmli buffer for 10 min, separated by SDS-PAGE, and immunoblotted using anti-HA, anti-SET, and anti-HMGB2 antibodies.
  • the cells were visualized using 503 Platform from Intelligent Imaging Innovations, under 40X and 63X oil immersion. 8 Z-stacks were taken per image at 1 um per step and the image were deconvolved using nearest neighbor algorithm. The images were processed using Slidebook version 5.
  • Network analysis was carried out using PPI data from Ingenuity, the STRING database (http://string.embl.de), and PPis found experimentally in published studies and in above-described SILAC experiments ( Li, Immunity, 2011, 35: 426-440 ; Boumeester, Nat Cell Biol, 2004, 6: 97-105 ; Rozenblatt-Rosen et al., Nature, 2012; 487(7408):491-5 ; ( Pichlmair et al., Nature, 2012 ; Cristea et al., J Virol, 2010, 84: 7803-7814 ).
  • Lysate preparation p53-/- MEFs were pelleted and then lysed in panel of lysis buffers.
  • NE-PER Pieris-PER (Pierce) was used following manufacturer recommendations to isolate cytoplasmic and nuclear fractions.
  • Cells were incubated in HLB (10 mM HEPES pH 7.4, 10mM KCl, 1 mM EDTA) containing protease inhibitors (Roche) for 10 min at 4°C followed by lysis for 1 min in HLB supplemented with 0.3% Triton X-100.
  • DNA pull-down assays p53-/- MEFs were stimulated with 1000U/mL interferon-beta (IFN) for 18 h or left untreated. Cytoplasmic extracts were prepared using HLB lysis (above). Biotinylated ISD (or buffer alone) and streptavidin beads were added to lysates, and samples were rotated for2.5 h at 4°C. Beads were pelleted and washed extensively with wash buffer (above). Precipitates were separated by SDS-PAGE, and stained with Coomassie blue (SimplyBlue SafeStain; Life Technologies).
  • IFN interferon-beta
  • the two samples were mixed, cysteines were reduced by DTT and alkylated with iodoacetamide, and proteins were eluted by heating in SDS sample buffer (Life Technologies) for 10 min before separation on a 4-12% gradient gel.
  • SDS sample buffer Life Technologies
  • the whole gel lane was cut into 8 slices, proteins were digested inside the gel with trypsin, and peptides were extracted from the gel as described4. Extracted peptides were purified with StageTips5 and analyzed with a 100 min acquisition method on a Thermo EASY-nLC 1OOO UHPLC coupled to a Q Exactive mass spectrometer.
  • MS/MS scans were acquired at a resolution of 70,000 with le6 AGC target and 5 ms maximum ion injection time, whereas MS/MS scans were acquired at alO resolution of 17,500 with 5e4 AGC target and 120 ms maximum ion injection time. Up to 12 MS/MS scans were triggered in a data dependent mode per duty cycle after peptide isolation with an isolation window of 2.5 m/z and HCD fragmentation at a normalized collision energy of 25.
  • Raw data files were processed in MaxQuant (v. 1.2.2.5)6 using the IPI mouse v3.68 as the search database. All proteins were identified with at least 2 or more unique peptides and quantified with 3 or more ratios.
  • SILAC ratios were normalized over the median of all protein ratios to correct for sample losses between parallel immunoprecipitation steps. To identify significant interactions, P-values were calculated via Gaussian modeling of the log(H/L) data, and proteins with P ⁇ 0.05 were designated as candidates for siRNA screening.
  • RNA microarray analysis 293T cells were stimulated with 1000 U/mL recombinant IFN followed by lysis 6 h later in RLT buffer (Qiagen). Total RNA was isolated using the RNeasy Mini kit (Qiagen). Genome-wide gene expression profiling was obtained by hybridizing the RNA to the Affymetrix Human U133 Plus 2.0 array. The cDNA synthesis, labeling, and subsequent hybridization to the microarrays were performed at the Molecular Profiling Laboratory, MGH Center for Cancer Research. (ii) p53-/- MEFs were treated with siRNAs for 72 h and then transfected with ISD. 6 h later, cells were lysed in RLT buffer. Each sample was performed in biological duplicates.
  • a set of candidate genes were generated from proteomic, genomic, and domain-based datasets that were hypothesized to contain unidentified ISD pathway components (FIG. IA).
  • PPI protein-protein interaction
  • Cytoplasmic extracts were prepared from mouse embryonic fibroblasts (MEFs) ( FIG. 8 ), and added biotinylated 45 base pair double-stranded DNA ('ISD' sequence) coupled to streptavidin beads as bait ( Stetson et al., Immunity, 2006, 24: 93-103 ).
  • SILAC stable isotope labeling by amino acids in cell culture
  • HMGBI HMGB family proteins
  • HMGBI HMGB2, HMGB3
  • IFI202B components of the AIM2 inflammasome
  • Roberts, Science, 2009, 323: 1057-1060 cytosolic RNA polymerase III complex
  • POLR3A, POLR3B, POLR3C, POLR3D, POLR3E, POLR3F, POLR3G, POLR3H, POLR IC, POLRID, POLR2E, POLR2H, and CRCP cytosolic RNA polymerase III complex
  • TREX I Three members of the SET complex (TREX I, APEX I, and HMGB2) were identified that regulate the ISD pathway as well as HIV-I detection and infection Yan et al., Nat Immunol, 2010, 11: 1005-1013 ; Stetson et al., Cell, 2008, 134: 587-598 ; Yanai et al, Nature, 2009, 462: 99-103 ; Yan et al., PLoS Pathog, 2009, 5: e1000327 ).
  • FIG. 9A A robust high-throughput siRNA (small interfering RNA) screening assay ( FIG. 9A ) was developed in which genes were knocked down in MEFs, the wells were stimulated with transfected dsDNA (ISD), and production of the IFN-inducible protein, CXCL1O, was measured by ELISA ( FIG. 2A ). Cell survival was measured after knockdown to control for cytotoxic effects of siRNA knockdown. The averages of triplicate wells are shown in FIG. 2B (also data not shown). Knockdown of selected hits was confirmed by qRT-PCR ( FIG. 9B ).
  • the ISD signaling pathway was divided broadly into three main processes: DNA sensing, primary signaling, and secondary (IFN) signaling ( FIG. 2C ).
  • DNA sensing a nucleic acid sensing pathway member that interacts with DNA ( Yanai et al, Nature, 2009, 462: 99-103 ).
  • Knockout of Hmgb2 reduced ISD-induced lfnbl and Cxcll 0 production 2-3 fold ( FIG.
  • the strongest A bcfl siRNA (si-1) was validated by cDNA rescue.
  • Abcfl is a cytosolic and ER-localized member of the ATP-Binding Cassette (ABC) family of transporters with a role in translational control ( Paytubi et al., Biol Chem, 2009, 284: 24061-24073 ), but unlike other members of this family, the Abcf subfamily genes lack transmembrane domains. Although a role in DNA sensing had not been previously observed, there is evidence that human polyomavirus 6 and 7 proteins interact with ABCF 1 ( Rozenblatt-Rosen et al., Nature, 2012; 487(7408):491-5 ), suggesting that this DNA virus may derive a benefit from targeting this node ( FIG. 2C ).
  • ABC ATP-Binding Cassette
  • CDC37 is a molecular chaperone that interacts with HSP90 to stabilize specific proteins, notably protein kinases ( Gray et al., Nat Rev Cancer, 2008, 8: 491-495 ), and is a putative interactor of TBK1 ( Li et al., Immunity, 2011, 35: 426-440 ; Boumeester et al., Nat Cell Biol, 2004: 97-105 ).
  • targeting the members of this complex with small molecules may block the ISD response by inhibiting TBK1 protein levels or activity, a phenotype that may be applicable to the treatment of certain autoimmune disorders (see below).
  • Secondary signaling downstream of the IFN receptor ( FIG. 2C ) is also important in the ISD response, and we identified known (e.g. IifJ and Statl) and previously unknown candidate mediators (e.g. Ptpnl ( Myers et al., J biol Chem, 2001, 276: 47771-47774 )) of the secondary signaling network ( FIGs. 2C and 11B ).
  • Knockout of the protein tyrosine phosphatase, PTPN 1 increased ISD-induced CXCLIO production 2.4-fold ( FIG. 4C and FIG. 11C ), validating the screening phenotype. Consistent with this result, small molecule inhibition of PTPN I increased CXCLIO production 9.1-fold in human MoDCs stimulated with ISD ( FIG. 4D ).
  • Targeting the two inhibitory phosphatases, PTPN I and PPP6C, by small molecules may serve as a way to enhance the immune response to certain DNA viruses and retroviruses (as described herein), and possibly to enhance the immunogenicity of DNA vaccines ( Ishikawa et al., Nature, 2009, 461: 788-792 ; Ishii, Nature, 2008, 45I : 725-729 ).
  • HMGB2 may function as a co-ligand for nucleic acid sensors though the precise role of HMGB2 has remained unclear ( Yanai et al, Nature, 2009, 462: 99-103 ). Itwas observed that not only HMGB2, but also IFI204 - apredicted DNA sensor also known as IFI16 ( Unterholzner et al., Nat. Rev. Immunol., 2010, 11: 997-1004 ) - was a candidate interactor of ABCF1 (FIGs. S B and C). The experiments show that that ABCF1 may interact with HMGB2, IFI16, and the SET complex.
  • Trexl-1-dependent autoimmunity and retroviral infection was further examined. While in culture Trexl-1- cells may not spontaneously produce type I IFNs or ISGs, retroviral infection of these cells induces IFN and ISG production in the absence of Trexl ( FIG. 13A and ( Yan et al., Nat Immunol, 2010, 11: lOOS - 1013 ). Major screening hits were knocked down in Trexl-1- MEFs and infected the cells with an HIV-based retrovirus. Knockdown of 4 of these genes (i.e.
  • Ptpnl, Tiparp, Mdpl, and Ppp6c significantly enhanced the ability of retroviral infection to induce IFN and ISG production ( P ⁇ O.OS), while knockdown of 12 of these genes (including Abcfl and Cdc37) as well as 4 known signal transduction components (i.e. Trim56, Sting, Tbkl, and Iif3) significantly abrogated the immune response ( P ⁇ O.OS; FIG. 6A-C and FIG. 13B ).
  • fibroblasts were cultured from a healthy control and a patient with Aicardi-Goutieres syndrome (AGS) who was compound heterozygote for mutations in the Trex 1 gene (R1 14H/D201ins). Cells were treated with vehicle alone or small molecule inhibitors and infected with retrovirus ( FIG. 7 ). Induction levels of Mx 1 were determined by qRT-PCR. Data was graphed as averages of triplicate wells ( FIG. 7 ). Small molecules were used at: 500 nM celastrol, 100 nM 17-DMAG, and 500 nM BX795 ( FIG. 7 ).
  • DNA-protein interaction, protein-protein interaction, and loss-of-function screening datasets were generated and used to identify new ISD pathway components; validated several of the newly identified components; demonstrated that a subset also function in the response to retroviral infection in Trexl-1- cells; and showed that small molecule inhibitors of several of these components can modulate the innate immune response to dsDNA and retroviral infection.
  • ABCFl As a cytoplasmic protein that associates with dsDNA, IFI16, and HMGB2, and regulates the interferon response to transfected dsDNA and retroviral infection. These results implicate ABCF 1 as a key component of the ISD pathway.
  • the experiments also identified SET complex members (SET, ANP32A, and HMGB2) as ABCFl interactors.
  • the SET complex contains three DNA nucleases (TREX 1, APEX I, and NME I); the chromatin-modifying proteins SET and ANP32A; and HMGB2, which functions as a co-receptor for nucleic acid receptors among other roles ( Chowdhury et al., Anuu Rev Immunol, 2008, 26: 389-420 ).
  • the interactions which were observed among dsDNA, ABCF I, HMGB2, and other SET complex members show that early steps in DNA recognition may occur at the ER-localized SET complex.
  • the complex member TREX I may prevent HIV-I DNA detection, and its absence may result in accumulation ofretroelement DNA at the ER which drives an ISD response ( Yan et al., Nat Immunol, 2010, 11: 1005-1013 ; Stetson et al., Cell, 2008, 134: 587-598 ; Yang et al., Cell, 2007, 131: 873-886 ). Furthermore, the complex members SET and NME I may also detect HIV-I DNA, and in turn regulate HIV-I infectivity ( Yan et al., PLoS Pathog, 2009, 5: eI000327 ).
  • the SET complex may recognize viral DNA as damaged DNA, specifically via its base excision repair (BER) activity and/or its distorted structure (e.g. HMGB2) ( Yan, Proc Natl Acad Sci USA, 2011108: 9244-9249 ). Consistent with this model, it was found that ISD interactors include the SET and BER complex member, APEX I, as well as nearly the entire BER complex (e.g. PARP I, PARP2, POLB, LIG3, XRCC I, FEN I, and PCNA). These results suggest that the SET complex plays a central role in DNA sensing and forms a coordinated system for detecting, modifying, and degrading viral or retroelement DNA.
  • BER base excision repair

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Claims (5)

  1. ABCF1-hemmende siRNA zur Verwendung in der Behandlung einer Erkrankung, die mit einem aberranten DNA-Erkennungsweg assoziiert ist, wobei es sich bei der mit einem aberranten DNA-Erkennungsweg assoziierten Erkrankung um eines aus Aicardi-Goutières-Syndrom (AGS), familiärem Chilblain-Lupus (FCL) und retinaler Vaskulopathie mit cerebraler Leukodystrophie (RVCL) handelt.
  2. ABCF1-Hemmer zur Verwendung nach Anspruch 1, wobei der Hemmer vor dem Auftreten von mit der Autoimmunerkrankung assoziierten Symptomen verabreicht wird.
  3. ABCF1-Hemmer zur Verwendung nach Anspruch 1, wobei das Subjekt, das die Behandlung empfängt, eine Trex1-Mutation trägt.
  4. ABCF1-Hemmer zur Verwendung nach einem der Ansprüche 1-3 in Kombination mit einem oder mehreren aus einem HSP90-Hemmer, einem CDC37-Hemmer, oder einem TBK1-Hemmer.
  5. ABCF1-Hemmer zur Verwendung nach Anspruch 4, wobei
    a) es sich beim HSP90-Hemmer um 17-DMAG, 17-AAG, Geldanamycin, oder Ganetespib handelt; und/oder
    b) es sich beim CDC37-Hemmer um Celastrol handelt; und/oder
    c) es sich beim TBK1-Hemmer um BX795 oder MRT67307 handelt.
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